Amplicon-based next-generation sequencing of plasma cell-free DNA for detection of driver and resistance mutations in advanced non-small cell lung cancer

Background

Genomic analysis of plasma cell-free DNA is transforming lung cancer care; however, available assays are limited by cost, turnaround time, and imperfect accuracy. Here, we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC).

Patients and methods

Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1, and other rare genotypes) were collected while on therapy and analyzed blinded to tumor genotype. Plasma NGS was carried out using enhanced tagged amplicon sequencing of hotspots and coding regions from 36 genes, as well as intronic coverage for detection of ALK/ROS1 fusions. Diagnostic accuracy was compared with plasma droplet digital PCR (ddPCR) and tumor genotype.

Results

A total of 168 specimens from 46 patients were studied. Matched plasma NGS and ddPCR across 120 variants from 80 samples revealed high concordance of allelic fraction (R2 = 0.95). Pretreatment, sensitivity of plasma NGS for the detection of EGFR driver mutations was 100% (30/30), compared with 87% for ddPCR (26/30). A full spectrum of rare driver oncogenic mutations could be detected including sensitive detection of ALK/ROS1 fusions (8/9 detected, 89%). Studying 25 patients positive for EGFR T790M that developed resistance to osimertinib, 15 resistance mechanisms could be detected including tertiary EGFR mutations (C797S, Q791P) and mutations or amplifications of non-EGFR genes, some of which could be detected pretreatment or months before progression.

Conclusions

This blinded analysis demonstrates the ability of amplicon-based plasma NGS to detect a full range of targetable genotypes in NSCLC, including fusion genes, with high accuracy. The ability of plasma NGS to detect a range of preexisting and acquired resistance mechanisms highlights its potential value as an alternative to single mutation digital PCR-based plasma assays for personalizing treatment of TKI resistance in lung cancer.

Assessment of Resistance Mechanisms and Clinical Implications in Patients With EGFR T790M-Positive Lung Cancer and Acquired Resistance to Osimertinib

Importance

Osimertinib mesylate is used globally to treat EGFR-mutant non-small cell lung cancer (NSCLC) with tyrosine kinase inhibitor resistance mediated by the EGFR T790M mutation. Acquired resistance to osimertinib is a growing clinical challenge that is poorly understood.

Objective

To understand the molecular mechanisms of acquired resistance to osimertinib and their clinical behavior.

Design, Setting, and Participants

Patients with advanced NSCLC who received osimertinib for T790M-positive acquired resistance to prior EGFR tyrosine kinase inhibitor were identified from a multi-institutional cohort (n = 143) and a confirmatory trial cohort (NCT01802632) (n = 110). Next-generation sequencing of tumor biopsies after osimertinib resistance was performed. Genotyping of plasma cell-free DNA was studied as an orthogonal approach, including serial plasma samples when available. The study and analysis were finalized on November 9, 2017.

Main Outcomes and Measures

Mechanisms of resistance and their association with time to treatment discontinuation on osimertinib.

Results

Of the 143 patients evaluated, 41 (28 [68%] women) had tumor next-generation sequencing after acquired resistance to osimertinib. Among 13 patients (32%) with maintained T790M at the time of resistance, EGFR C797S was seen in 9 patients (22%). Among 28 individuals (68%) with loss of T790M, a range of competing resistance mechanisms was detected, including novel mechanisms such as acquired KRAS mutations and targetable gene fusions. Time to treatment discontinuation was shorter in patients with T790M loss (6.1 vs 15.2 months), suggesting emergence of pre-existing resistant clones; this finding was confirmed in a validation cohort of 110 patients with plasma cell-free DNA genotyping performed after osimertinib resistance. In studies of serial plasma levels of mutant EGFR, loss of T790M at resistance was associated with a smaller decrease in levels of the EGFR driver mutation after 1 to 3 weeks of therapy (100% vs 83% decrease; P = .01).

Conclusions and Relevance

Acquired resistance to osimertinib mediated by loss of the T790M mutation is associated with early resistance and a range of competing resistance mechanisms. These data provide clinical evidence of the heterogeneity of resistance in advanced NSCLC and a need for clinical trial strategies that can overcome multiple concomitant resistance mechanisms or strategies for preventing such resistance.

Ultra-deep next-generation sequencing of plasma cell-free DNA in patients with advanced lung cancers: results from the Actionable Genome Consortium

BACKGROUND

Noninvasive genotyping using plasma cell-free DNA (cfDNA) has the potential to obviate the need for some invasive biopsies in cancer patients while also elucidating disease heterogeneity. We sought to develop an ultra-deep plasma next-generation sequencing (NGS) assay for patients with non-small-cell lung cancers (NSCLC) that could detect targetable oncogenic drivers and resistance mutations in patients where tissue biopsy failed to identify an actionable alteration.

PATIENTS AND METHODS

Plasma was prospectively collected from patients with advanced, progressive NSCLC. We carried out ultra-deep NGS using cfDNA extracted from plasma and matched white blood cells using a hybrid capture panel covering 37 lung cancer-related genes sequenced to 50 000× raw target coverage filtering somatic mutations attributable to clonal hematopoiesis. Clinical sensitivity and specificity for plasma detection of known oncogenic drivers were calculated and compared with tissue genotyping results. Orthogonal ddPCR validation was carried out in a subset of cases.

RESULTS

In 127 assessable patients, plasma NGS detected driver mutations with variant allele fractions ranging from 0.14% to 52%. Plasma ddPCR for EGFR or KRAS mutations revealed findings nearly identical to those of plasma NGS in 21 of 22 patients, with high concordance of variant allele fraction (r = 0.98). Blinded to tissue genotype, plasma NGS sensitivity for de novo plasma detection of known oncogenic drivers was 75% (68/91). Specificity of plasma NGS in those who were driver-negative by tissue NGS was 100% (19/19). In 17 patients with tumor tissue deemed insufficient for genotyping, plasma NGS identified four KRAS mutations. In 23 EGFR mutant cases with acquired resistance to targeted therapy, plasma NGS detected potential resistance mechanisms, including EGFR T790M and C797S mutations and ERBB2 amplification.

CONCLUSIONS

Ultra-deep plasma NGS with clonal hematopoiesis filtering resulted in de novo detection of targetable oncogenic drivers and resistance mechanisms in patients with NSCLC, including when tissue biopsy was inadequate for genotyping.

Discrimination of Germline EGFR T790M Mutations in Plasma Cell-Free DNA Allows Study of Prevalence Across 31,414 Cancer Patients

Purpose: Plasma cell-free DNA (cfDNA) analysis is increasingly used clinically for cancer genotyping, but may lead to incidental identification of germline-risk alleles. We studied EGFR T790M mutations in non-small cell lung cancer (NSCLC) toward the aim of discriminating germline and cancer-derived variants within cfDNA.Experimental Design: Patients with EGFR-mutant NSCLC, some with known germline EGFR T790M, underwent plasma genotyping. Separately, deidentified genomic data and buffy coat specimens from a clinical plasma next-generation sequencing (NGS) laboratory were reviewed and tested.Results: In patients with germline T790M mutations, the T790M allelic fraction (AF) in cfDNA approximates 50%, higher than that of EGFR driver mutations. Review of plasma NGS results reveals three groups of variants: a low-AF tumor group, a heterozygous group (∼50% AF), and a homozygous group (∼100% AF). As the EGFR driver mutation AF increases, the distribution of the heterozygous group changes, suggesting increased copy number variation from increased tumor content. Excluding cases with high copy number variation, mutations can be differentiated into somatic variants and incidentally identified germline variants. We then developed a bioinformatic algorithm to distinguish germline and somatic mutations; blinded validation in 21 cases confirmed a 100% positive predictive value for predicting germline T790M. Querying a database of 31,414 patients with plasma NGS, we identified 48 with germline T790M, 43 with nonsquamous NSCLC (P < 0.0001).Conclusions: With appropriate bioinformatics, plasma genotyping can accurately predict the presence of incidentally detected germline risk alleles. This finding in patients indicates a need for genetic counseling and confirmatory germline testing. Clin Cancer Res; 23(23); 7351-9. ©2017 AACR.

Abstract 4112: Overgrowth of competing resistance mechanisms, such as an acquired KRAS mutation, underlies a poor prognosis subtype of acquired resistance to osimertinib in T790M-positive NSCLC

Introduction: Osimertinib is a third-generation EGFR tyrosine kinase inhibitor (TKI) which is highly active in EGFR-mutant NSCLC with resistance to prior EGFR TKI. Acquired resistance to osimertinib had been observed clinically; an improved understanding of the molecular mechanisms of resistance is needed. Methods/Results: We initially studied an institutional cohort of 86 patients (pts) treated with osimertinib for advanced T790M-positive NSCLC. 50 pts had progressed on therapy, of whom 25 underwent a resistance biopsy and 17 had NGS results available. 6 pts maintained the T790M mutation at resistance, of whom 3 also acquired an EGFR C797S mutation. The remaining 11 pts had loss of T790M, of whom 5 had evidence of a competing resistance mechanism: 2 with histologic transformation to SCLC, one with BRAF V600E, one with an FGFR3-TACC fusion, and one with KRAS Q61K. For the final case, we confirmed the acquired KRAS Q61K on therapy using serial plasma genotyping. Time to treatment failure (TTF) on osimertinib was 3 months median in pts with loss of T790M and 14 months median in pts with maintained T790M. To test the hypothesis that loss of T790M is a poor prognosis subtype of resistance, we analyzed 127 pts treated for T790M-positive NSCLC on the phase I AURA trial of osimertinib. Plasma drawn after progression was submitted for genotyping using droplet digital PCR. 88 pts had a detectable EGFR driver mutation and were eligible for resistance analysis. 45 pts (51%) had detectable T790M at resistance, 17 (19%) of whom also acquired a C797S mutation; the remaining 43 pts (49%) had loss of T790M and no C797S. Median TTF on osimertinib was 6 months in pts with loss of T790M and 11 months in pts with maintained T790M; among pts with TTF &lt;5 months, 72% had loss of T790M. To study whether baseline plasma genotyping could predict the eventual pattern of resistance on osimertinib, we studied 30 pts from the AURA trial with pretreatment plasma genotyping positive for T790M and an EGFR driver. The relative allelic fraction (AF) of T790M was calculated as the ratio of the T790M AF to the driver AF. In 9 pts with eventual loss of T790M, the relative T790M AF trended lower (25% median) than in 21 pts with maintained T790M at resistance (38% median, P = 0.086). Conclusion: Different molecular mechanisms of acquired resistance to osimertinib have different clinical presentations, with early resistance being associated with loss of T790M and the potential for overgrowth of a competing resistance mutation. These findings have implications in steering pts towards suitable trials for overcoming resistance - pts with early resistance to osimertinib could favor trials targeting a competing resistance mechanisms (e.g. MET inhibition) while pts with late resistance could favor trials targeting EGFR C797S.

Citation Format: Geoffrey R. Oxnard, Yuebi Hu, Philip Tracy, Nora Feeney, Cloud P. Paweletz, Kenneth S. Thress, Pasi A. Janne. Overgrowth of competing resistance mechanisms, such as an acquired KRAS mutation, underlies a poor prognosis subtype of acquired resistance to osimertinib in T790M-positive NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4112. doi:10.1158/1538-7445.AM2017-4112

Prospective Validation of Rapid Plasma Genotyping for the Detection of EGFR and KRAS Mutations in Advanced Lung Cancer

IMPORTANCE

Plasma genotyping of cell-free DNA has the potential to allow for rapid noninvasive genotyping while avoiding the inherent shortcomings of tissue genotyping and repeat biopsies.

OBJECTIVE

To prospectively validate plasma droplet digital PCR (ddPCR) for the rapid detection of common epidermal growth factor receptor (EGFR) and KRAS mutations, as well as the EGFR T790M acquired resistance mutation.

DESIGN, SETTING, AND PARTICIPANTS

Patients with advanced nonsquamous non-small-cell lung cancer (NSCLC) who either (1) had a new diagnosis and were planned for initial therapy or (2) had developed acquired resistance to an EGFR kinase inhibitor and were planned for rebiopsy underwent initial blood sampling and immediate plasma ddPCR for EGFR exon 19 del, L858R, T790M, and/or KRAS G12X between July 3, 2014, and June 30, 2015, at a National Cancer Institute-designated comprehensive cancer center. All patients underwent biopsy for tissue genotyping, which was used as the reference standard for comparison; rebiopsy was required for patients with acquired resistance to EGFR kinase inhibitors. Test turnaround time (TAT) was measured in business days from blood sampling until test reporting.

MAIN OUTCOMES AND MEASURES

Plasma ddPCR assay sensitivity, specificity, and TAT.

RESULTS

Of 180 patients with advanced NSCLC (62% female; median [range] age, 62 [37-93] years), 120 cases were newly diagnosed; 60 had acquired resistance. Tumor genotype included 80 EGFR exon 19/L858R mutants, 35 EGFR T790M, and 25 KRAS G12X mutants. Median (range) TAT for plasma ddPCR was 3 (1-7) days. Tissue genotyping median (range) TAT was 12 (1-54) days for patients with newly diagnosed NSCLC and 27 (1-146) days for patients with acquired resistance. Plasma ddPCR exhibited a positive predictive value of 100% (95% CI, 91%-100%) for EGFR 19 del, 100% (95% CI, 85%-100%) for L858R, and 100% (95% CI, 79%-100%) for KRAS, but lower for T790M at 79% (95% CI, 62%-91%). The sensitivity of plasma ddPCR was 82% (95% CI, 69%-91%) for EGFR 19 del, 74% (95% CI, 55%-88%) for L858R, and 77% (95% CI, 60%-90%) for T790M, but lower for KRAS at 64% (95% CI, 43%-82%). Sensitivity for EGFR or KRAS was higher in patients with multiple metastatic sites and those with hepatic or bone metastases, specifically.

CONCLUSIONS AND RELEVANCE

Plasma ddPCR detected EGFR and KRAS mutations rapidly with the high specificity needed to select therapy and avoid repeat biopsies. This assay may also detect EGFR T790M missed by tissue genotyping due to tumor heterogeneity in resistant disease.

Abstract 5192: Utilizing NSCLC PDXs derived from patients on osimertinib (AZD9291) clinical trials to further refine therapeutic strategies

Background: Osimertinib (AZD9291)is a mutant-selective EGFR tyrosine kinase inhibitor (TKI) effective against EGFR activating and the T790M acquired resistance mutations.Osimertinib has been approved by the US FDA for patients with EGFR T790M positive NSCLC with resistance to first line EGFR TKIs. However, as acquired resistance to osimertinib is now emerging, we aimed to develop PDXs from patients with: a) acquired resistance to first-line EGFR TKIs prior to enrolling on osimertinib trials and b) post-osimertinib resistance.

Methods: Pre- and post-osimertinib tumor biopsies were implanted into the flank or sub-renal capsule of NSG mice. Successfully established PDXs were expanded and confirmed by ddPCR and NGS to maintain molecular fidelity to the original patient tumor. The osimertinib efficacy in a subset of PDX models was tested and compared to clinical osimertinib response in the patients from whom the PDXs were derived. Acquired osimertinib resistance models were further treated with a panel of novel targeted agent combinations, matching the potential mechanism of osimertinib resistance.

Results: 46 patients underwent a pre-osimertinib or post-osimertinib biopsy. 26 biopsies were from the AURA trial for patients with acquired resistance to first-line EGFR TKIs; 5 biopsies were from the TATTON trial for patients without a T790M mutation; and 7 biopsies were from patients with acquired resistance to osimertinib. A platform of 16 PDX models have been successfully developed and shown to exhibit diverse mechanisms of TKI resistance as confirmed by NGS. These models include: 6 with EGFR T790M; 4 with EGFR non-T790M resistance to erlotinib; and 4 with acquired resistance to osimertinib. In the drug efficacy studies, PDX sensitivity to osimertinib is shown to be comparable to the corresponding patient's clinical response. In the DFCI-243 model (patient: EGFR T790M+, PR 8.9 months), tumors showed regression during the dosing phase and rapidly regrew upon cessation of osimertinib treatment. In contrast, in the DFCI-217 model (patient EGFR T790M+, PR &gt;24 months), tumors showed sustained regression even after osimertinib treatment cessation. In the DFCI-284, a potential model of primary AZD9291 resistance tumors showed no regressions with osimertinib treatment. PDX models have also been used to refine treatment approaches for acquired resistance to osimertinib. DFCI-306 model established from a patient who developed an acquired BRAF mutation while on osimertinib has been shown to respond to either selumetinib or the selumetinib/osimertinib combination.

Conclusion: We have developed a platform of NSCLC PDXs from patients with acquired resistance to first-line EGFR TKIs and the newly approved third-generation inhibitor osimertinib. These models can be used to refine treatment strategies in patients with acquired resistance to first-line EGFR TKIs with primary or acquired resistance to osimertinib.

Citation Format: Sangeetha Palakurthi, Man Xu, Amanda J. Redig, Michael Dills, Prafulla Gokhale, Jinyun Choi, Atsuko Ogino, Yanan Kuang, Nora Feeney, Cloud Paweletz, Paul Kirscmeier, Jessie English, Darren Cross, Pasi Jänne. Utilizing NSCLC PDXs derived from patients on osimertinib (AZD9291) clinical trials to further refine therapeutic strategies. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5192.

Abstract 3157: Serial droplet digital PCR (ddPCR) of plasma cell-free DNA (cfDNA) as pharmacodynamic (PD) biomarker in Phase 1 clinical trials for patients (pts) with KRAS mutant non-small cell lung cancer (NSCLC)

Introduction: Phase 1 clinical trials of novel therapeutics have historically focused on toxicity, but increasingly are doubling as efficacy studies in biomarker-enriched populations. Given the small sample sizes (∼3-6 patients per dose), response on imaging may be a coarse marker of therapeutic effect. Here we piloted serial ddPCR of plasma cfDNA as a PD marker in a phase I combination study of a MEK inhibitor and a CDK 4/6 inhibitor in patients with RAS mutated cancers.

Methods / Results: Twenty-five pts with RAS-mutated cancer (incl. 17 patients with KRAS-mutant NSCLC) have been enrolled to date in a phase I dose escalation trial of the MEK inhibitor PD-0325901 with the CDK4/6 inhibitor palbociclib (NCT02022982). Plasma for cfDNA genotyping was collected at baseline prior to therapy and at the beginning of cycle 2. Plasma genotyping for KRAS G12X mutations was performed using a validated and highly quantitative droplet digital PCR assay.

Pts were enrolled in 5 dose level cohorts ranging from 75 mg palbociclib daily (3 weeks on, 1 week off) with 2 mg PD-0325901 BID (3 weeks on 1week off) to 125 mg palbociclib daily with 8 mg PD-0325901 BID (Table). KRAS mutations were detected in 14/24 pts at baseline (59%, median 1402 copies/mL plasma, range: 11-93000), consistent with the previously reported sensitivity of 64%. A second blood draw at cycle 2 was obtained for all 14 pts. A positive plasma response, defined as decrease of KRAS G12X mutants from first to second dose, was observed in 6 pts (range -6% - -100%) with the most plasma responders (n = 4 pts) at the maximum administered dose. At lower administered doses, there was a median increase in plasma KRAS mutant levels.

Conclusions: Increasing dose levels resulted in more consistent decreases in KRAS mutation in cfDNA, consistent with a dose-dependent pharmacodynamic effect.These results highlight the potential value of serial plasma ddPCR as a PD marker in early phase clinical trials. Dose LevelPalbociclib (QD, 3 wks on 1 wk off) mgPD-0325901 (BID, 3 wks on 1 wk off) mgN Enrolled (N analyzed)Median Plasma change KRAS mut(%)17523 (1)+2427543 (3)+60 (range +31 - +150)310048 (4)+150 (range -6 - +341)412544 (2)+9 (range -45 - +61)512587 (4)-27 (range -7 - -43)

Citation Format: Cloud P. Paweletz, Geoffrey R. Oxnard, Nora Feeney, John F. Hilton, Leena Gandhi, Khanh T. Do, Adrienne Anderson, Andrew Wolanski, Alexander Tejeda, Jessie M. English, Paul T. Kirschmeier, Pasi A. Jänne, Geoffrey I. Shapiro. Serial droplet digital PCR (ddPCR) of plasma cell-free DNA (cfDNA) as pharmacodynamic (PD) biomarker in Phase 1 clinical trials for patients (pts) with KRAS mutant non-small cell lung cancer (NSCLC). [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3157.

A Prospective Evaluation of Circulating Tumor Cells and Cell-Free DNA in EGFR-Mutant Non-Small Cell Lung Cancer Patients Treated with Erlotinib on a Phase II Trial

PURPOSE

Genotype-directed therapy is the standard of care for advanced non-small cell lung cancer (NSCLC), but obtaining tumor tissue for genotyping remains a challenge. Circulating tumor cell (CTC) or cell-free DNA (cfDNA) analysis may allow for noninvasive evaluation. This prospective trial evaluated CTCs and cfDNA in EGFR-mutant NSCLC patients treated with erlotinib until progression.

EXPERIMENTAL DESIGN

EGFR-mutant NSCLC patients were enrolled in a phase II trial of erlotinib. Blood was collected at baseline, every 2 months on study, and at disease progression. Plasma genotyping was performed by droplet digital PCR for EGFR19del, L858R, and T790M. CTCs were isolated by CellSave, enumerated, and analyzed by immunofluorescence for CD45 and pan-cytokeratin and EGFR and MET FISH were also performed. Rebiopsy was performed at disease progression.

RESULTS

Sixty patients were enrolled; 44 patients discontinued therapy for disease progression. Rebiopsy occurred in 35 of 44 patients (80%), with paired CTC/cfDNA analysis in 41 of 44 samples at baseline and 36 of 44 samples at progression. T790M was identified in 23 of 35 (66%) tissue biopsies and 9 of 39 (23%) cfDNA samples. CTC analysis at progression identified MET amplification in 3 samples in which tissue analysis could not be performed. cfDNA analysis identified T790M in 2 samples in which rebiopsy was not possible. At diagnosis, high levels of cfDNA but not high levels of CTCs correlated with progression-free survival.

CONCLUSIONS

cfDNA and CTCs are complementary, noninvasive assays for evaluation of acquired resistance to first-line EGFR TKIs and may expand the number of patients in whom actionable genetic information can be obtained at acquired resistance. Serial cfDNA monitoring may offer greater clinical utility than serial monitoring of CTCs. Clin Cancer Res; 22(24); 6010-20. ©2016 AACR.

Abstract A105: Credentialing the concept of “co-clinical trials”: Utility of lung cancer PDX models derived from patients on AZD9291 clinical trials

Background: The EGFR T790M mutation is the most common mechanism of acquired drug resistance to currently approved EGFR inhibitors gefitinib, erlotinib, and afatinib. AZD9291 is a mutant-selective EGFR inhibitor effective against both EGFR activating and T790M mutations while sparing wild type EGFR. AZD9291 is highly active in patients with lung cancer with the EGFR T790M mutation, with a response rate of 61% and progression free survival of ∼10 months. However, as resistance to AZD9291 is beginning to emerge, we aimed to develop patient derived xenografts (PDXs) using pre-treatment biopsies obtained from patients with acquired resistance to first-line EGFR inhibitors enrolling on clinical trials with AZD9291. These clinically annotated PDX models allow direct correlation with the clinical efficacy of AZD9291 in patients and may be useful in studying mechanisms of acquired resistance to AZD9291 and refine strategies for treatments.

Methods: Pre-AZD9291 treatment tumor biopsies (core needle biopsies or pleural effusions) were implanted into the flank or sub-renal capsule of NSG mice. Tumors were serially passed in NSG mice for up to 3 generations. Successfully established models were expanded and treated with AZD9291. The efficacy in the PDX model was compared to the clinical efficacy of AZD9291 in the patient from whom the model was derived.

Results: 33 patients underwent a pre-AZD9291 treatment biopsy (26 core needle; 7 pleural effusions). 26/33 patients enrolled in the AURA AZD9291 clinical trial for patients with acquired resistance to first-line EGFR inhibitors. From these patients, 10 PDX models have been successfully developed so far and confirmed by ddPCR to maintain fidelity to the original patient tumor's EGFR mutation status. These models include 6 with EGFR T790M and 4 with EGFR non-T790M mechanisms of resistance to erlotinib. Among the 10 patients used to develop PDX models, the best clinical response to AZD9291 included 5 partial responses, 3 progressive diseases, 1 stable disease and 1 acquired resistance. A subset of these PDX models were further tested for their sensitivity to AZD9291 and the data was consistent with the clinical responses of the patients. Two models, DFCI 243 and DFCI 217 (both with EGFR T790M; both patients with PR &gt; 9 months) were treated with gefitinib (6.25mg/kg) or AZD9291 (25 mg/kg). Both models were confirmed to maintain EGFR T790M and had a dramatic response to AZD9291 but not to gefitinib treatment. However, tumors rapidly regrew upon cessation of AZD9291 treatment. DFCI 306 PDX model established from a patient with acquired resistance to monotherapy with AZD9291, showed AZD9291 resistance in vivo. AZD9291 treatment of DFCI 284, a model with EGFR T790M derived from a patient with primary resistance to AZD9291, is underway.

Conclusion: We have developed PDXs from patients with erlotinib resistance who were treated with AZD9291. The PDX platform is currently being utilized in studies to refine strategies to: a) improve durability of responses to AZD9291 in EGFR T790M mutation positive patients and b) identify combinations in EGFR T790M mutation positive or negative patients who have de novo or acquired resistance to AZD9291.

Citation Format: Sangeetha S. Palakurthi, Man Xu, Amanda Redig, Michael Dills, Prafulla Gokhale, Jihyun Choi, Atsuko Ogino, Yanan Kuang, Nora Feeney, Cloud Paweletz, Paul Kirschmeier, Jessie English, Darren Cross, Pasi A. Janne. Credentialing the concept of “co-clinical trials”: Utility of lung cancer PDX models derived from patients on AZD9291 clinical trials. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A105.

Pulmonary Embolism

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